![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Apr 22, 2019:
- 11:57 PM Ticket #1879 (ChimeraX does not start on Windows 10) closed by
- fixed: Disabled use of "-X faulthandler" which makes things work again when …
- 5:57 PM Ticket #1883 (Open command "vseries true" option does not work with Amira files) created by
- The vseries option to the open command is supposed to treat the …
- 5:51 PM Ticket #1882 (Show errors that occur before main window started in GUI log) created by
- When an error occurs before the main window is shown the error goes to …
- 5:46 PM Ticket #1881 (Clicking Model panel show button on volume does not show it) created by
- With AICS_10-136.ome.tif clicking the show button on channel 4 (model …
- 5:43 PM Ticket #1880 (Have macOS installer dmg show arrow to drag ChimeraX to Applications) created by
- At the ChimeraX microscopy tutorial I found another user running …
- 4:06 PM Ticket #1879 (ChimeraX does not start on Windows 10) created by
- […]
- 3:09 PM Ticket #1878 (Smarter handling of ATOM/HETATM column 21) created by
- Column 21 of ATOM/HETATM records is not officially assigned a meaning …
- 2:26 PM ChangeLog edited by
- (diff)
- 11:08 AM Ticket #1877 (measure buriedArea syntax documentation problem) closed by
- fixed
- 8:20 AM Ticket #1877 (measure buriedArea syntax documentation problem) created by
- […]
Apr 21, 2019:
- 5:59 PM Ticket #1865 (rerunning BLAST from same instance of tool puts unformatted data at ...) closed by
-
fixed: Fixed in 3e4701234.
The
bootgridtable was used … - 4:33 PM Ticket #1864 (BLAST results show parameter settings different from blast command ...) closed by
- fixed: Fixed in 7ae130f8. The BLAST search parameters are now …
Apr 19, 2019:
- 11:52 AM Ticket #1876 (Allow writing OME TIFF files containing multichannel optical ...) created by
- Would like to be able to write out optical microscopy data including …
- 11:40 AM Ticket #1875 (Allow creating multiple marker sets) created by
- Currently the marker placement mouse mode always adds markers to the …
- 8:41 AM Ticket #1874 (ISOLDE: isolde/libmolc.so: undefined symbol) created by
- […]
Apr 18, 2019:
- 8:17 PM Ticket #1870 ("measure volume" when style isn't surface gives TypeError: Array ...) closed by
- fixed: Fixed. Surface that never had geometry set was giving error when …
- 8:04 PM Ticket #1873 (Volume series surface disappears when histogram threshold moved) closed by
- fixed: Fixed. Problem was the volume surface associated with each histogram …
- 8:03 PM Ticket #1873 (Volume series surface disappears when histogram threshold moved) created by
- Saw in today's 3d microscopy workshop at Parnassus that after changing …
- 7:19 PM Ticket #1838 (Session close/reset: NameError: name 'task' is not defined) closed by
- fixed: Fixed in 1922f9e15 Fix multiple bugs introduced by …
- 6:34 PM Ticket #1871 (Graphics window gray after first model opened.) closed by
- fixed: Fixed. If resize event arrives before ui.main_window set then we …
- 5:57 PM Ticket #1872 (RFE: visual indicator on mouse-mode icons for which mode is active) created by
- Since the right-button mouse modes are mutually exclusive, it would be …
- 5:36 PM Ticket #1871 (Graphics window gray after first model opened.) created by
- […]
- 5:10 PM Ticket #1870 ("measure volume" when style isn't surface gives TypeError: Array ...) created by
- Although it is a user error to try to use "measure volume" when the …
- 3:32 PM Ticket #1852 (Unable to render images despite nogui/offscreen) closed by
- fixed: A couple of bugs where quashed: (1) PyOpenGL wasn't loading the OSMesa …
- 3:28 PM Ticket #1735 (AddH fails after residue deletion) closed by
- fixed: Problem only occurs if SEQRES records (or mmCIF equivalent) are …
- 2:54 PM ChangeLog edited by
- (diff)
- 2:22 PM Ticket #1858 (Blast Protein should not list nucleic chains as possible queries) closed by
- fixed: Fixed in 2db95f5ae. Only amino acid chains are listed now.
- 1:28 PM Ticket #1859 (Blast Protein should not launch when return pressed in numerical field) closed by
- fixed: Fixed. Return key now takes you to the next field except for the …
- 1:13 AM Ticket #1869 (Crash trying to demote Chain to Sequence) created by
- […]
Apr 17, 2019:
- 5:20 PM Ticket #1866 (Installing ISOLDE: 'utf-8' codec can't decode byte 0xa0 in position ...) closed by
- duplicate
- 4:41 PM Ticket #1868 (Error switching to volume plane style with multichannel data) closed by
- fixed: Fixed. Volume viewer saw volume region switch to single plane and …
- 4:29 PM Ticket #1868 (Error switching to volume plane style with multichannel data) created by
- […]
- 2:53 PM Ticket #1867 (Errors restoring session with TIFF stacks or directly opening them) created by
- […]
- 1:46 PM Ticket #1866 (Installing ISOLDE: 'utf-8' codec can't decode byte 0xa0 in position ...) created by
- […]
- 12:42 PM Ticket #1863 (Shell useless after most errors) closed by
- duplicate: Duplicate of #1802; adding you to cc list for that
- 12:35 PM Ticket #470 (Multiple copies of shell tool) closed by
- fixed: Some previous change has fixed this -- I'm not sure what!
- 12:03 PM Ticket #1865 (rerunning BLAST from same instance of tool puts unformatted data at ...) created by
- I don't know if this is widget flakiness and/or lack of clearing …
- 11:57 AM Ticket #1864 (BLAST results show parameter settings different from blast command ...) created by
- Probably doesn't matter which structure, but I had 2ahj open and used …
- 11:49 AM Ticket #1863 (Shell useless after most errors) created by
- […]
- 11:16 AM Ticket #1862 (Some funkiness installing wheels needing tilde expansion) created by
- […]
- 10:28 AM Ticket #1861 (OpenMM crash) created by
- […]
- 10:16 AM Ticket #1860 (Blast Protein results widget flaky? (sometimes no horizontal scroll)) created by
- This may or may not be reproducible but on some of my Blast Protein …
- 10:13 AM Ticket #1859 (Blast Protein should not launch when return pressed in numerical field) created by
- Causes inadvertent premature launching, especially bad when searching …
- 10:07 AM Ticket #1858 (Blast Protein should not list nucleic chains as possible queries) created by
- Summary says it all. For example if I have 6cmn open, the choices of …
- 9:55 AM Ticket #1857 (RFE: Blast Protein ability to show alignment for any subset of hits in ...) created by
- This is an important feature of Chimera's Blast Protein. Otherwise …
- 9:38 AM Ticket #1856 (OpenGL error, glClear: invalid framebuffer operation) created by
- […]
- 1:26 AM Ticket #1855 (Can't set 'vertices' attribute on Drawing) created by
- […]
Apr 16, 2019:
- 1:23 PM Ticket #1851 (OpenGL error drawing selection: glBlitFramebuffer -- invalid operation) closed by
- nonchimerax: VMware opengl problem drawing selection outline.
- 1:00 PM Ticket #1852 (Unable to render images despite nogui/offscreen) reopened by
- well the bugreporting error is fixed, but not the other part
- 12:59 PM Ticket #1852 (Unable to render images despite nogui/offscreen) closed by
- fixed: fixed by Tom G
- 12:58 PM Ticket #1853 (test bug reporting) closed by
- not a bug
- 12:53 PM Ticket #1854 (Error reporting a bug when http proxy used) closed by
- fixed: Fixed. Only happened when http proxy set. Import was at wrong indent …
- 12:51 PM Ticket #1854 (Error reporting a bug when http proxy used) created by
- Begin forwarded message: From: James Starlight Subject: Re: …
- 12:48 PM Ticket #1850 (ParmEd) closed by
- not a bug: I guess I'm closing this for now then!
- 12:47 PM Ticket #1853 (test bug reporting) created by
- […]
- 12:38 PM Ticket #1852 (Unable to render images despite nogui/offscreen) created by
- […]
- 5:01 AM Ticket #1851 (OpenGL error drawing selection: glBlitFramebuffer -- invalid operation) created by
- […]
Apr 15, 2019:
- 7:34 PM Ticket #1571 (Undo selection buggy) closed by
- fixed: Fixed in 979d57d40. Problem was that updating the …
- 6:03 PM Ticket #1661 (Support adding state managers from bundles) closed by
- fixed: New API implemented and committed 040c391a4.
- 4:27 PM Ticket #1850 (ParmEd) created by
- I’m going to need to start using ParmEd (part of the AmberTools suite, …
- 3:45 PM Ticket #1848 (Clipper not a supported wheel on this platform) closed by
- not a bug: This is just simple user error. The only people who have access to …
- 3:44 PM Ticket #1849 (String decoding of BLAST results no longer necessary) closed by
- fixed: Conrad fixed this yesterday
- 3:15 PM Ticket #1847 (Either: Tempy broken, or Registration internal error -- dealer's choice) closed by
- duplicate: dup of #1846
- 3:06 PM Ticket #1849 (String decoding of BLAST results no longer necessary) created by
- […]
- 1:05 PM Ticket #1848 (Clipper not a supported wheel on this platform) created by
- […]
- 12:09 PM Ticket #1847 (Either: Tempy broken, or Registration internal error -- dealer's choice) created by
- […]
- 12:06 PM Ticket #1846 (Either: Tempy broken, or Registration internal error -- dealer's choice) created by
- […]
- 6:48 AM Ticket #1845 ("toolshed install" errors reporting to status bar rather than log) created by
- Related to #1819, in recent builds all the warnings and traceback when …
Apr 12, 2019:
- 4:02 PM ChangeLog edited by
- (diff)
- 4:01 PM Ticket #1483 (Allow web service request to be blocking) closed by
- fixed: Fixed in 3bad659e3. Added blocking keyword to …
- 10:41 AM Ticket #1844 (Toolshed cache KeyError crashes startup from app icon) created by
- […]
- 7:28 AM Ticket #1843 (Move selected models uses wrong coordinates if parent model moved in scene) created by
- If I open an NMR ensemble and apply some transform to the group: …
Apr 11, 2019:
- 6:07 PM Ticket #1800 (error reading DICOM CT: TypeError: Cannot cast ufunc multiply output) closed by
- fixed: Fixed. Problem was with floating point dicom scaling factor applied …
- 5:50 PM Ticket #1801 (error reading DICOM RTDOSE: tuple object not callable) closed by
- fixed: Fixed. Typo in new dicom plane reading code that only effect data …
- 5:19 PM Ticket #1799 (error reading DICOM SEG models: IndexError: tuple index out of range) closed by
- fixed: Fixed. New code to read dicom maps a plane at a time didn't properly …
- 4:35 PM Ticket #1842 (Session save: Unable to restore objects of ImageDrawing class in ...) created by
- […]
- 1:00 PM Ticket #1841 (Wrong vertex indices in wavefront OBJ files with multiple objects) closed by
- fixed: Fixed.
- 1:00 PM Ticket #1841 (Wrong vertex indices in wavefront OBJ files with multiple objects) created by
- Saving an OBJ file with multiple models uses face vertex indices that …
- 12:03 PM Ticket #1823 (saved image silhouette width too fat) reopened by
- I think in all case the user really does want the silhouette width and …
- 11:44 AM Ticket #232 (Model panel slows down movie recording) closed by
- wontfix: I don't think 1a0m ever draws that fast anymore. Having never opened …
- 10:34 AM Ticket #1839 (Modeller interface option using wrong settings name) closed by
- fixed
Apr 10, 2019:
- 7:03 PM Ticket #1796 (Some kind of crash on the GPU) closed by
- nonchimerax: MacBook Pro 15,3 graphics driver crash, macOS mojave, AMD Radeon Pro …
- 6:17 PM Ticket #1812 (Changing lighting of MRC volume: 'numpy.float64' object cannot be ...) closed by
- duplicate: Fixed. Duplicate of #1600.
- 5:48 PM Ticket #1818 (Normals incorrect for instanced objects different scaling along each axis) closed by
- wontfix: You are right the graphics rendering assumes the Model position is …
- 5:29 PM Ticket #1821 (surface-center marker placement: cannot import name 'surface' from ...) closed by
- fixed
- 5:25 PM Ticket #1823 (saved image silhouette width too fat) closed by
- not a bug: Silhouette width is specified in pixels. If an image is saved with …
- 5:05 PM Ticket #1828 (2dlabels: Too many arguments to QFont() call) closed by
- duplicate: Duplicate. Fixed long ago.
- 4:57 PM Ticket #1829 (Views restored from sessions: self.positions key is None) closed by
- fixed: Fixed. I believe this bug is caused by making a named view, then …
- 4:36 PM Ticket #1830 ('vop' alias not known/registered with only molmap (and not 'volume') ...) closed by
- fixed: Fixed. vop is an alias for the volume command and it was not being …
- 2:46 PM ChangeLog edited by
- (diff)
- 12:08 PM Ticket #1840 (Session restore with BILD objects: Unable to restore objects of ...) created by
- […] c1.0_drawing.bild
- 11:23 AM Ticket #1839 (Modeller interface option using wrong settings name) created by
- […]
Apr 9, 2019:
- 4:13 PM Ticket #1838 (Session close/reset: NameError: name 'task' is not defined) created by
- […]
- 2:44 PM Ticket #1837 (modeller cannot use template that differs from its associated sequence) closed by
- fixed: Fixed by same change that fixed #1834
- 2:20 PM Ticket #1837 (modeller cannot use template that differs from its associated sequence) created by
- Example open …
- 12:55 PM Ticket #1834 (Modeller backend failure) closed by
- fixed: Code assumed that chain associations started at the beginning of the …
- 11:02 AM Ticket #1836 ("toolshed uninstall": JSONDecodeError) created by
- […]
- 8:44 AM Ticket #760 (ChimeraX/Isolde error: can't import clipper) closed by
- fixed: Cleaning up old ticket - ISOLDE and Clipper have been available for …
- 8:42 AM Ticket #1279 (Problem installing Clipper bundle) closed by
- not a bug: Just cleaning up old tickets.
- 8:41 AM Ticket #1328 (User-supplied template CYX does not match the residue 60 (CYS)) closed by
- fixed: Ancient ticket, long since fixed.
- 8:41 AM Ticket #1774 (Various errors) closed by
- fixed: If ISOLDE's gui panel is closed when a simulation is running, it now …
Apr 8, 2019:
- 5:25 PM Ticket #1833 (Modeller: Item in 'polymeric_res_names' arg is not a string) closed by
- fixed: Okay, there is not _inherent_ restriction of the number of model when …
- 3:48 PM Ticket #1335 (Python testing scripts: 'session' not available) closed by
- fixed: testing scripts renamed to cxtest.py
- 3:46 PM Ticket #1616 (Session restore: msgpack: max_ext_len exceeded) closed by
- fixed: Fixed!
- 3:41 PM Ticket #1831 (Bundles registering file formats are always imported on startup) closed by
- fixed: Added has_(open|export)_func() that tests for existence of …
- 3:23 PM Ticket #1825 (mmCIF 6mit hangs) closed by
- fixed: Added timeout to fetch_file. Using a minute as the default, and 15 …
- 3:22 PM Ticket #1835 (ISOLDE installation: UnicodeDecodeError) closed by
- duplicate: Workaround already in ISOLDE FAQ
- 3:18 PM Ticket #1835 (ISOLDE installation: UnicodeDecodeError) created by
- […]
- 2:44 PM Ticket #1834 (Modeller backend failure) created by
- […] dimer-monomer-super.cxs
- 1:01 PM Ticket #1833 (Modeller: Item in 'polymeric_res_names' arg is not a string) created by
- […] nhase-modeling.cxs
- 11:54 AM Ticket #937 (Allow color command to color by atom properties) closed by
- fixed: "color byattribute" implemented awhile back now
- 11:24 AM Ticket #1832 (auto-seq-struct association only happens if sequence opened first) created by
- Automatic association happens if the sequence alignment is opened …
- 11:00 AM Ticket #1831 (Bundles registering file formats are always imported on startup) created by
- Bundles registering file formats are always imported on startup even …
Apr 7, 2019:
- 8:53 PM Ticket #1830 ('vop' alias not known/registered with only molmap (and not 'volume') ...) created by
- […]
- 3:38 PM Ticket #1829 (Views restored from sessions: self.positions key is None) created by
- […] cartoon-stepV2.cxs
Apr 6, 2019:
Apr 5, 2019:
- 1:33 PM Ticket #1661 (Support adding state managers from bundles) reopened by
- Implementation was incorrect because it always initialized providers …
- 11:37 AM Ticket #1827 (Allow toolshed to be queried for providers) created by
- A manager may wish to know all possible providers, rather than simply …
- 11:32 AM Ticket #1826 ('Session' object has no attribute 'preset_mgr') closed by
- duplicate: Hi Julia, This problem was fixed about a month ago, so if you get a …
- 10:11 AM Ticket #1824 (Qt crash) closed by
- can't reproduce
- 5:24 AM Ticket #1826 ('Session' object has no attribute 'preset_mgr') created by
- […]
- 4:33 AM Ticket #1825 (mmCIF 6mit hangs) created by
- […]
- 12:39 AM Ticket #1824 (Qt crash) created by
- […]
Apr 4, 2019:
- 4:29 PM Ticket #1823 (saved image silhouette width too fat) created by
- If I save a smaller image than the window the silhouettes become much …
- 3:17 PM 2019-04-04 created by
- 2:11 PM DeveloperMeetings edited by
- (diff)
Apr 3, 2019:
- 10:46 AM Ticket #1821 (surface-center marker placement: cannot import name 'surface' from ...) created by
- […]
- 10:42 AM Ticket #1820 (Matchmaker for specific selections) closed by
- not a bug: Okay, win-win. :-)
- 7:13 AM Ticket #1820 (Matchmaker for specific selections) created by
- Working on adding reference model-based restraints to ISOLDE - I have …
- 6:31 AM Ticket #1819 (Problem with PyPI dependencies (or dependencies of dependencies?)) created by
- I've just recently added the PyPI package ParmEd (for working with and …
- 1:39 AM Ticket #1818 (Normals incorrect for instanced objects different scaling along each axis) created by
- Context is a new "adaptive" distance restraint scheme (see …
Apr 2, 2019:
- 1:28 PM Ticket #1817 (Save log as commands) created by
- Extract and save commands from log
- 1:27 PM Ticket #1816 (Restore log contents from sessions) created by
- Use dated disclosure triangle to hide/show previous work. Trick is to …
- 1:07 PM Ticket #1784 (Spurious "command replacing existing command" log entries) closed by
- fixed: Greg apparently fixed this.
- 1:06 PM Ticket #1661 (Support adding state managers from bundles) closed by
- fixed: Implemented in 895143f2c45. Added Managers, Manager, …
- 1:03 PM Ticket #1327 (Tethers not hidden correctly) closed by
- fixed: Fixed in ec5804859. Tethers were always displayed for …
Apr 1, 2019:
- 5:39 PM Ticket #1813 (Header sequence restore: missing 1 required positional argument: ...) closed by
- duplicate: Fixed on 2/27
- 5:36 PM Ticket #1811 (Header sequence restore: missing 1 required positional argument: ...) closed by
- duplicate: Fixed on 2/27
Mar 29, 2019:
- 10:18 AM Ticket #1815 (style selAtom gives keyword error) created by
- In particular "style selAtom & nucleic ringFill on" fails with …
- 9:41 AM Ticket #1814 (missing cartoon tethers to nucleotides) created by
- Repeat by opening 2bna and switching all atoms with "nuc atoms" and …
- 9:03 AM Ticket #1813 (Header sequence restore: missing 1 required positional argument: ...) created by
- […]
- 8:48 AM Ticket #1812 (Changing lighting of MRC volume: 'numpy.float64' object cannot be ...) created by
- […]
- 7:30 AM Ticket #1811 (Header sequence restore: missing 1 required positional argument: ...) created by
- […]
Mar 27, 2019:
- 5:10 PM Ticket #1767 (AddH: trying to bind bonded geometry of atom with no bonds) closed by
- fixed: When finding H-bonds, skip donors/acceptors missing heavy-atom bond …
- 11:28 AM Ticket #1809 (Qt crash) closed by
- can't reproduce: Hi Paul, Thank you so much for providing details about what you were …
- 7:57 AM Ticket #1810 (Morph: ValueError: models have different number of chains) created by
- […]
Mar 26, 2019:
- 7:04 PM Ticket #1809 (Qt crash) created by
- […] phospholipide-eau.cxs
- 10:50 AM Ticket #1808 (self._positions is None) closed by
- duplicate
- 10:50 AM Ticket #1807 (self._positions is None) closed by
- duplicate
- 10:48 AM Ticket #1806 (self._positions is None) closed by
- duplicate
- 10:47 AM Ticket #1805 (Qt crash) closed by
- can't reproduce
- 10:34 AM Ticket #1804 (Error in AddH error message :-)) closed by
- fixed
- 10:27 AM Ticket #1803 (Tab completion failing on session.view) closed by
- nonchimerax: Apparently tab completion doesn't work on properties. 'view' is a …
- 8:17 AM Ticket #1808 (self._positions is None) created by
- […]
- 7:40 AM Ticket #1807 (self._positions is None) created by
- […]
- 7:37 AM Ticket #1806 (self._positions is None) created by
- […]
- 7:27 AM Ticket #1805 (Qt crash) created by
- […]
- 7:08 AM Ticket #1804 (Error in AddH error message :-)) created by
- […]
- 4:09 AM Ticket #1803 (Tab completion failing on session.view) created by
- Not sure if it's related to #1802 or not, but there's some weirdness …
- 3:25 AM Ticket #1802 (Python shell: tab completion produces "KeyError: 'matches' " after ...) created by
- […]
Mar 25, 2019:
- 4:19 PM 2019-03-21 edited by
- (diff)
- 4:10 PM 2019-03-21 edited by
- (diff)
- 11:59 AM Ticket #1801 (error reading DICOM RTDOSE: tuple object not callable) created by
- for example, any of the RT DOSE subdirs in the same dataset as …
- 11:56 AM Ticket #1800 (error reading DICOM CT: TypeError: Cannot cast ufunc multiply output) created by
- for example, the CT subdirectory in the same dataset as attached to …
- 11:46 AM Ticket #1798 ('Session' object has no attribute 'preset_mgr') closed by
- duplicate: Hi Klaas, This problem was fixed the day after the version you …
- 11:14 AM Ticket #1799 (error reading DICOM SEG models: IndexError: tuple index out of range) created by
- Reading these files was working fine for a while, but another change …
- 11:02 AM Ticket #1797 ('Session' object has no attribute 'preset_mgr') closed by
- duplicate: Hi Kuen, This problem was fixed the day after the version you got(!), …
Mar 24, 2019:
Mar 23, 2019:
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